Data of RNA-Seq in fetal lung exposed to diesel exhaust particle
This dataset reflects the RNA sequencing in ex vivo fetal lungs collected from ICR mice at an age of 11.5 embryonic (E) days exposed to diesel exhaust particles (DEP) at 0 (control group) and 50 μg/mL (DEP group) for 3 days. The dataset includes the summary of the gene sequenced, differentially expressed genes (DEG), and genes annotated by Disease Ontology (DO), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways.
Steps to reproduce
Ex vivo fetal lungs were collected after exposure to DEPs at 0 (control) and 50 μg/mL for 3 days and homogenized in TRIzol® (Invitrogen, Waltham, MA, USA). RNA extraction and purification were done by SimpliNano-Biochrom Spectrophotometer (Biochrom, MA, USA). RNA integrity and degradation were examined via Qsep 100 DNA/RNA Analyzer (BiOptic Inc., Taiwan). RNA quality was examined via FastQC and MultiQC (Marioni et al., 2008). HISAT2 software (v 2.1.0) was used to read pairs from each sample were aligned to the reference genome (Mus musculus, GRCm39). The reads numbers mapped to individual genes were counted via FeatureCounts (v 2.0.0). Trimmed Mean of M-values normalization (TMM) was performed via differentially expressed genes (DEG)seq (v 1.40.0) for gene expression without biological duplicate. Relative Log Expression normalization (RLE) was performed via DESeq2 (v 1.26.0) for gene expression with biological duplicate. The resulting p-values were adjusted using the Benjamini and Hochberg’s approach for controlling the FDR. Gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and DEGs enrichment analysis were conducted by clusterProfiler (v 3.14.3).